imodfillin(1) General Commands Manual imodfillin(1)
NAME
imodfillin - fill in missing contours in IMOD model using mesh data
SYNOPSIS
imodfillin [options] input_model output_model
DESCRIPTION
imodfillin will fill in contours in an IMOD model on sections that were
skipped during modeling. It interpolates a contour between existing
ones using information in the object mesh created by imodmesh. Each
interpolated contour will fall on the surface connecting existing con-
tours. It is thus necessary to run imodmesh before imodfillin.
Since you need to have a mesh between contours on non-adjacent sec-
tions, you should use one or more imodmesh options to connect across
gaps in the data. If sections have either a complete set of contours
or no contours at all, then the -s option will suffice. If the pattern
is less rigid than this, use the -P option in addition (or exclu-
sively), where the number of passes that you specify with this option
equals the maximum number of sections of separation between contours
that you wish to connect. Do not use any imodmesh option that would
set the z increment to greater than 1 (i.e., -l,-i, or -z ), for then
imodfillin will probably create contours on sections that already have
them.
By default, the program will attempt to fill in all closed-contour
objects that have meshes, but will skip open-contour objects. Use the
-o option to specify a subset of objects to be done, or to force it to
do particular open-contour objects.
The created contours will inherit any surface or time information con-
tained in the meshes. If your original contours have surface numbers,
be sure to mesh with the -S option to preserve this surface information
in the meshes, so that the interpolated contours will have the same
surface numbers as the original ones.
OPTIONS-e Place new contours in existing objects. Use this option if you
do not plan to check and modify the interpolated contours.
-n Place new contours in new objects; this is the default, so that
contours can be checked conveniently. One new object will be
created for each object that is being filled in. These contours
may be moved into the proper object either one by one or all at
once via the Edit-Contour-Move dialog and M hotkey in 3dmod.
-olist
Do operations only on objects in the list of numbers. The list
can consist of comma-separated ranges (e.g., 1,7-11,13-17,19).
Without this option, all closed contour objects with meshes are
filled in.
-ivalue
Set the Z increment for filling in contours. This option has
two effects: the program will fill in only gaps that are wider
than the given value, and it will insert new contours at this
given Z increment instead of on every section.
-Rvalue
Resolution or tolerance for point reduction in the generated
contours. Points are eliminated if they are within this dis-
tance of the lines connecting the remaining points, just as with
the -R option in imodmesh. Values in the range 0.25 to 0.5
are often useful.
FILES
If the model file already exists, it becomes a backup file with ~ added
to its name.
AUTHOR
David Mastronarde
SEEALSO3dmod, imodmeshBUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.10.25 imodfillin(1)